File naming/organization could still be an issue… the current-generation of Plex scanners/agents are usually better than the legacy agents… but they also tend to be more strict when it comes to naming. So if your QNAP used to run based on those old agents, a new setup using the new agents might still run into some trouble.
That being said… this can be a likely scenario for your tv-shows… it shouldn’t have that big of an impact on a movie library.
As for permissions… can you confirm for what DSM account you’ve granted access to your media? DSM 6 and 7 are very different when it comes to that. There’s still a log of older guides out there referring to the old DSM 6 approach.
If it’s none of those, your server logs might show some pointers as for why those other files aren’t being picked up.
